ReorderSam.ReorderSamReferenceArgumentCollection (picard 2.18.2 API)

java.lang.Object
- picard.sam.ReorderSam.ReorderSamReferenceArgumentCollection

All Implemented Interfaces:: ReferenceArgumentCollection

Enclosing class:: ReorderSam

public static class ReorderSam.ReorderSamReferenceArgumentCollection
extends Object
implements ReferenceArgumentCollection

- Field Summary
  
  Fields
  Modifier and Type Field Description
  
  File REFERENCE
- Constructor Summary
  
  Constructors
  Constructor Description
  
  ReorderSamReferenceArgumentCollection()
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method Description
  
  File getReferenceFile()
  - Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Fields
Modifier and Type	Field	Description
`File`	`REFERENCE`

Constructors
Constructor	Description
`ReorderSamReferenceArgumentCollection()`

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`File`	`getReferenceFile()`

Field Detail

REFERENCE

@Argument(shortName="R",
          common=false,
          doc="Reference sequence to reorder reads to match.  A sequence dictionary corresponding to the reference fasta is required.  Create one with CreateSequenceDictionary.")
public File REFERENCE

Constructor Detail
- ReorderSamReferenceArgumentCollection
```
public ReorderSamReferenceArgumentCollection()
```

Method Detail
- getReferenceFile
```
public File getReferenceFile()
```
  Specified by:
  
  getReferenceFile in interface ReferenceArgumentCollection
  
  Returns:
  
  The reference provided by the user, if any, or the default, if any.

Class ReorderSam.ReorderSamReferenceArgumentCollection

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

REFERENCE

Constructor Detail

ReorderSamReferenceArgumentCollection

Method Detail

getReferenceFile